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SOS -- MuTect is picking up obvious germline mutations

Haiying7Haiying7 Heidelberg, GermanyMember

This is the command I used to run MuTect:
/usr/bin/java -Xmx4g -Djava.io.tmpdir=tmp -jar ${MuTect}mutect-1.1.7.jar \
--input_file:normal ${BQSR_dir}${Blood}.recal.bam --input_file:tumor ${BQSR_dir}${Nevus}.recal.bam \
--out ${MuTect_dir}${Blood}${Nevus}_call_stats.out \
--coverage_file ${MuTect_dir}${Blood}
${Nevus}coverage.wig.txt \
--vcf ${MuTect_dir}${Blood}
${Nevus}.vcf \
--analysis_type MuTect --reference_sequence ${GATK_hg} --cosmic ${COSMIC} --dbsnp ${dbSNP} --intervals ${Intervals} \
--disable_auto_index_creation_and_locking_when_reading_rods \
--min_qscore 30 --max_alt_alleles_in_normal_count 0

The results got more somatic mutations than when I run exactly same command except that I dropped the last line. So I went through all IGVs, and found that some somatic mutations identified are obviously germline mutations!
I have attached some figures.

I feel so anxious. I don't have an idea how to debug this. Please any one help me.

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